Modifier and Type | Method and Description |
---|---|
static String |
AminoAcidPattern.getTaggedModifiedSequence(PtmSettings modificationProfile,
AminoAcidPattern aminoAcidPattern,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g, <mox>.
|
String |
AminoAcidSequence.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
String |
AminoAcidPattern.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g, <mox>.
|
static String |
AminoAcidSequence.getTaggedModifiedSequence(PtmSettings modificationProfile,
String sequence,
HashMap<Integer,ArrayList<String>> confidentModificationSites,
HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
static String |
AminoAcidSequence.getTaggedResidue(char residue,
String modificationName,
PtmSettings modificationProfile,
int localizationConfidenceLevel,
boolean useHtmlColorCoding,
boolean useShortName)
Returns the single residue as a tagged string (HTML color or PTM tag).
|
Modifier and Type | Method and Description |
---|---|
static ArrayList<NeutralLoss> |
IonFactory.getNeutralLosses(PtmSettings ptmSettings)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
|
static HashSet<Integer> |
IonFactory.getReporterIons(PtmSettings ptmSettings)
Returns the reporter ions to annotate with the given PTM settings.
|
Modifier and Type | Method and Description |
---|---|
String |
ModificationFactory.convertPridePtm(String pridePtmName,
PtmSettings modProfile,
ArrayList<String> unknownPtms,
boolean isFixed)
Tries to convert a PRIDE Modification to utilities Modification name, and add it to the
modification profile.
|
Modifier and Type | Method and Description |
---|---|
String |
Peptide.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g, <mox>.
|
String |
Peptide.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g, <mox>.
|
static String |
Peptide.getTaggedModifiedSequence(PtmSettings modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> confidentModificationSites,
HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g, <mox>.
|
Modifier and Type | Method and Description |
---|---|
String |
Tag.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean includeTerminalGaps)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
String |
Tag.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedModifications,
boolean includeTerminalGaps)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
static String |
Tag.getTaggedModifiedSequence(PtmSettings modificationProfile,
Tag tag,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedPtms,
boolean includeTerminalGaps)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateModifications(Peptide peptide,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Verifies that the definition of every modification name is available.
|
Constructor and Description |
---|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PtmSettings ptmSettings,
PeptideVariantsParameters peptideVariantsPreferences)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
PtmSettings |
XTandemParametersDialog.getModificationProfile()
Returns the modification profile corresponding to the input by the user.
|
Constructor and Description |
---|
XTandemParametersDialog(Dialog owner,
Frame parent,
XtandemParameters xtandemParameters,
PtmSettings modificationProfile,
double fragmentIonMassAccuracyInDa,
boolean editable)
Creates new form XtandemParametersDialog with a dialog as owner.
|
XTandemParametersDialog(Frame parent,
XtandemParameters xtandemParameters,
PtmSettings modificationProfile,
double fragmentIonMassAccuracyInDa,
boolean editable)
Creates new form XtandemParametersDialog with a frame as owner.
|
Constructor and Description |
---|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
PtmSettings modificationProfile)
Deprecated.
use the panel with ion selection instead
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
PtmSettings modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
PtmSettings modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
Modifier and Type | Method and Description |
---|---|
PtmSettings |
SearchParameters.getPtmSettings()
Returns the PTM settings.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PtmSettings.equals(PtmSettings otherProfile)
Returns true of the two profiles are identical.
|
void |
SearchParameters.setPtmSettings(PtmSettings ptmSettings)
Sets the PTM settings.
|
Constructor and Description |
---|
PtmSettings(PtmSettings ptmSettings)
Constructor creating a new Modification profile based on the given one.
|
Modifier and Type | Method and Description |
---|---|
void |
OmssaParameters.setPtmIndexes(PtmSettings modificationProfile)
Set the PTM indexes of the modifications searched.
|
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